Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019543.1 Corchorus olitorius cultivar O-4 contig19576, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 30821
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:735 original size:15 final size:15
Alignment explanation
Indices: 715--769 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
705 AGAAGATGAT
715 GGCACC-AACATCGAC
1 GGCACCGAA-ATCGAC
*
730 GGCACCGAAATTGAC
1 GGCACCGAAATCGAC
*
745 GGCACCGAAGAT-GAT
1 GGCACCGAA-ATCGAC
760 GGCACCGAAA
1 GGCACCGAAA
770 CTGATGACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 1 0.03
15 31 0.86
16 4 0.11
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (15 bp):
GGCACCGAAATCGAC
Found at i:774 original size:15 final size:15
Alignment explanation
Indices: 730--824 Score: 102
Period size: 15 Copynumber: 6.3 Consensus size: 15
720 CAACATCGAC
* *
730 GGCACCGAAATTGAC
1 GGCACCGAAACTGAT
745 GGCACCGAAGA-TGAT
1 GGCACCGAA-ACTGAT
760 GGCACCGAAACTGAT
1 GGCACCGAAACTGAT
* *
775 GACACCAAAACTGAT
1 GGCACCGAAACTGAT
790 GGCACCGAAACTGAT
1 GGCACCGAAACTGAT
* * * *
805 GTCACCAAAATTGAC
1 GGCACCGAAACTGAT
820 GGCAC
1 GGCAC
825 TAAGGATGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
14 1 0.01
15 66 0.97
16 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (15 bp):
GGCACCGAAACTGAT
Found at i:794 original size:45 final size:45
Alignment explanation
Indices: 706--812 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
696 TGTCATGGAA
* * *
706 GAAGATGATGGCACCAACATCGACGGCACCGAAATTGACGGCACC
1 GAAGATGATGGCACCAACATCGACGACACCAAAACTGACGGCACC
* *
751 GAAGATGATGGCACCGAA-A-CTGATGACACCAAAACTGATGGCACC
1 GAAGATGATGGCACC-AACATC-GACGACACCAAAACTGACGGCACC
*
796 GAA-ACTGATGTCACCAA
1 GAAGA-TGATGGCACCAA
813 AATTGACGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 4 0.08
45 47 0.89
46 2 0.04
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.13
Consensus pattern (45 bp):
GAAGATGATGGCACCAACATCGACGACACCAAAACTGACGGCACC
Found at i:2768 original size:49 final size:48
Alignment explanation
Indices: 2691--2819 Score: 152
Period size: 49 Copynumber: 2.7 Consensus size: 48
2681 CAAGCAATCC
* * * *
2691 TTTACTTTTCACTGCACTTTTTCACAATTTTTACCACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAACACAAAATTGAACT
* * *
2739 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTTAACACAAAATTGAACT
* *
2788 TTTAATTTTCATCGCACTTTTTATCAATTTTT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTT
2820 TGACAAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 5 0.07
48 22 0.32
49 35 0.51
50 6 0.09
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (48 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTAACACAAAATTGAACT
Found at i:4288 original size:84 final size:85
Alignment explanation
Indices: 4197--4353 Score: 262
Period size: 85 Copynumber: 1.9 Consensus size: 85
4187 AAATATATTT
4197 AAAAATTCTAATATATCTAA-ATTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT
1 AAAAATTCTAATATATCTAAGATTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT
4261 AAAGAGATTAGATTTAATTA
66 AAAGAGATTAGATTTAATTA
* * ** *
4281 AAAAATTCTGATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAACTAAAATAGTTAT
1 AAAAATTCTAATATATCTAAGATTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT
4346 AAAGAGAT
66 AAAGAGAT
4354 AAAAGATATT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 19 0.28
85 48 0.72
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (85 bp):
AAAAATTCTAATATATCTAAGATTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT
AAAGAGATTAGATTTAATTA
Found at i:4988 original size:12 final size:12
Alignment explanation
Indices: 4967--5006 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
4957 TTTGCGATCG
4967 AATTTGCAACCA
1 AATTTGCAACCA
*
4979 ATATTT-CAACTA
1 A-ATTTGCAACCA
4991 AATTTGCAACCA
1 AATTTGCAACCA
5003 AATT
1 AATT
5007 AATACTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (12 bp):
AATTTGCAACCA
Found at i:5384 original size:2 final size:2
Alignment explanation
Indices: 5371--5403 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5361 TCTTGTAGTG
*
5371 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5404 GACAAGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11103 original size:14 final size:14
Alignment explanation
Indices: 11084--11112 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11074 GTCCATGTAC
11084 AAACTAATATTTTT
1 AAACTAATATTTTT
11098 AAACTAATATTTTT
1 AAACTAATATTTTT
11112 A
1 A
11113 TTTTATTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AAACTAATATTTTT
Found at i:12660 original size:25 final size:25
Alignment explanation
Indices: 12621--12671 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
12611 ACATAGACCA
12621 TCCACCGGAACAACTAATTTTTTGG
1 TCCACCGGAACAACTAATTTTTTGG
* *
12646 TCCACCTGAAGAACTAATTTTTTGG
1 TCCACCGGAACAACTAATTTTTTGG
12671 T
1 T
12672 AGCATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (25 bp):
TCCACCGGAACAACTAATTTTTTGG
Found at i:16132 original size:23 final size:23
Alignment explanation
Indices: 16106--16154 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
16096 AGAAATTTAG
* * *
16106 CTTTATAGAGTTGATTGTTTAAA
1 CTTTATAGAGATGACTATTTAAA
16129 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
16152 CTT
1 CTT
16155 AGAAATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:29984 original size:16 final size:16
Alignment explanation
Indices: 29965--30023 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
29955 CGGGCTCGGG
29965 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
29981 CGGGCTT-GGGT-TATGT
1 CGGG-TTCGGGTAT-TTT
29997 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
30013 CGGGCTCGGGT
1 CGGGTTCGGGT
30024 CGGGTTCGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.08
16 30 0.83
17 3 0.08
ACGTcount: A:0.05, C:0.15, G:0.42, T:0.37
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:30189 original size:13 final size:12
Alignment explanation
Indices: 30166--30212 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
30156 AAGTTTATTG
30166 ATAATATATAAT
1 ATAATATATAAT
30178 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
30191 ATAACAT-TATT
1 ATAATATATAAT
30202 ATCAATATATA
1 AT-AATATATA
30213 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:30502 original size:31 final size:33
Alignment explanation
Indices: 30467--30538 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
30457 TAAATTATTG
*
30467 CAAATTAAAAT-AAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAATAAAATGAAAGTC-TTAAATTAAA
*
30498 CAAA-T-AATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAAAATAAAATGAAAGTCTTAAATTAAA
30529 CAAATTAAAA
1 CAAATTAAAA
30539 GCTGATAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
29 3 0.09
30 5 0.15
31 21 0.64
32 2 0.06
33 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (33 bp):
CAAATTAAAATAAAATGAAAGTCTTAAATTAAA
Done.